Perkin, who was born in Sudbury (in the London Boroughs of Brent and Harrow), was the elder son of the famous chemist who discovered the aniline dyes, also called William Henry Perkin. As a child he assisted his father in his private laboratory. He was educated at the City of London School and then in 1877 followed his father to the Royal College of Chemistry. He then went to Germany where he studied at the universities of Würzburg and Munich. On his return to England he worked at Manchester before being appointed professor of chemistry at Heriot-Watt College, Edinburgh, in 1887. In 1892 he returned to Manchester as professor of organic chemistry and in 1912 he became Waynflete Professor of Chemistry at Oxford.

Perkin was a very practical chemist who, in a long career, achieved many syntheses and analyses. His first success came in his student days in Munich. It had been argued by Victor Meyer in 1876 that no ring with fewer than six carbon atoms could exist. Perkin succeeded in 1884 in preparing rings with four carbon atoms.

Of the many molecules he synthesized are the terpenes, limonene (1904), the oxygenated terpineol (1904), and camphoric acid (1903). He worked on many alkaloids, including strychnine and on natural coloring compounds like brazilin. Perkin also worked with William Pope, showing that optical activity can be found in compounds in which the carbon atoms are not necessarily asymmetrical.

He produced three chemical works in collaboration with Frederic Kipping and also did much to stimulate the growth of chemistry at Oxford by campaigning for the new laboratories that were opened there in 1922.